The [approximately 40] troops will bolster security at the embassy and help non-emergency personnel leave, said Samantha Reho, a spokeswoman from U.S. Africa Command.
“This contingent brought in several vehicles solely for use in protecting the embassy,” Reho said. She declined to provide any information about what military service or units the troops come from, citing operational security concerns.
“We do not discuss the specific forces involved or the specific capabilities the Crisis Response Force has available,” she said. “What I can say is the CRF is a flexible and ready force that has all the tools it needs to respond to any crisis in AFRICOM's area of responsibility.”
We have a Marine Corps force in Spain on call for this kind of mission and the story is in Marine Corps Times, so I'll go out on a ledge and say Marines--who traditionally defend State Department facilities overseas--provided the force.
Although I do believe we have a small force of Army infantry in Djibouti, too (last year it was a battalion but I think a smaller force rotated in), which is probably providing a company of infantry just in case:
An additional 130 military personnel currently in Djibouti are also prepared to provide support as necessary, the White House said.
Although it could mean special forces, since we're talking Djibouti.
UPDATE: The forces from Djibouti will be forward deployed to Uganda.